CEA – Civil Engineering Department

CHEME – Chemistry for Engineers

MODULE 3

SOIL CHEMISTRY

Soil is the top layer of the earth’s crust where organic matter grows. Many components, such
as pH, nutrient level, and organic content, determine a soil type. These factors can vary depending
on the type of plant or crop that grows in the soil and geographic location. The best way to
determine soil quality is by conducting a soil test.

SOIL

Gardeners know that you cannot grow vegetables just anywhere. The quality of vegetables grown
depends on the condition of the soil. Soil is the top layer of the Earth’s surface suitable for plant
growth. Although it is often referred to as dirt or ground, there is much more to soil than meets the
eye.

pH

One of the most essential components of soil is the pH. The pH of the soil can be modified by adding
different chemicals. Soil pH indicates how acidic or alkaline the soil is. The pH of the soil is crucial
because crops grow best in a narrow pH range, which can vary among crops. For example,
blueberries and a few types of flowers grow best when the pH is 5.5 or less. Potatoes, a more
familiar crop, grow best with a soil pH range of 5.5 to 6.0. Most garden vegetables, shrubs, trees,
and lawns grow best when the soil pH is over 6.0 or 6.5. The range between 5.5 and 7.5 is favorable
for two reasons. It allows sufficient microorganisms to break down organic matter. It is also the
best range for nutrient availability.

LIMING

The pH of the soil can be increased by liming. This is why people sometimes spread white powder
on their lawns or gardens. This white powder is lime. Calcitic limestone (CaCO3) provides a good
source of Calcium (Ca) and helps neutralize soil acidity. Dolomitic limestone functions similarly but
also adds Magnesium (Mg). The best limestone will have the greatest calcium and magnesium
content and be ground into tiny particles. The smaller particles allow the limestone to correct soil
acidity more rapidly. The chemistry to liming is quite simple. Hydrogen ions (H+) are attracted to
soil and organic material with a negative (-) charge. When lime is applied, these hydrogen ions are
exchanged for calcium or magnesium (Ca2+ or Mg2+) ions with a greater positive charge.

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 CEA – Civil Engineering Department
CHEME – Chemistry for Engineers

This helps to neutralize the acidity of the soil. The free hydrogen ions are taken out of the solution.
This also helps to increase the pH. This reaction demonstrates the process of liming:

Sometimes, the soil may have very high pH and need to be more acidic. This can be done using
sulfur, aluminum sulfate, or ammonium sulfate.

NUTRIENTS

Each year, the soil undergoes a series of cycles in which materials are added and taken away.
Organic matter and nutrients, in various forms, are constantly being added to the soil. Nutrients are
the minerals required by plants to survive. Plants must receive all the needed nutrients. There are
a total of sixteen elements required for plant growth. Each is necessary in different amounts. The
most important nutrients are called macronutrients. Nutrients that are essential but only needed in
small quantities are called micronutrients. Carbon, Hydrogen, and Oxygen are the big three
macronutrients. These are obtained almost unlimited amounts from the atmosphere and the water
around the plant. The other macronutrients are nitrogen (N), phosphorus (P), potassium (K),
calcium (Ca), magnesium (Mg), and sulfur (S). These nutrients should be available for plant uptake
from the soil. Micronutrients are obtained from the soil. They are boron (B), copper (Cu), chlorine
(Cl), iron (Fe), manganese (Mn), molybdenum (Mo), and zinc (Zn). They are all essential because
the absence of these will cause the plant to grow poorly or develop disease.

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 CEA – Civil Engineering Department
CHEME – Chemistry for Engineers

MACRONUTRIENTS

MINERAL

1. HYDROGEN, OXYGEN AND CARBON

✓ Plants and animals primarily comprise carbon, hydrogen, and oxygen. Plants obtain carbon and
oxygen from the air (as CO2 and O2) and hydrogen and oxygen from water (H2O). With the help of
light energy, they recombine these three elements into carbohydrates. This happens in the leaves
of plants during photosynthesis:

6CO2 + 6H2O + light energy → C6H12O6 + 6O2

✓ Carbon, hydrogen, and oxygen also combine to form hydrocarbons, the long molecular chains
that makeup fats, and the same three elements combine with nitrogen to form the main structure
of proteins. These three elements are key components of the large organic molecules that comprise
all living beings.

✓ Carbon also plays a crucial role in global climate change, as increased CO2 and CH4 (methane)
levels in the atmosphere (along with water vapor and a few other gases) reflect infrared radiation
to the earth, overall increasing the average surface temperature. Ecologists and soil scientists have
been examining the potential for building up soil organic matter to sequester C, removing it from
the atmosphere and maintaining it in the soil.

NON MINERAL

2. NITROGEN (N)

✓ Physiological role in plant development Plants take up nitrogen as the ammonium ion (NH4+) or
nitrate (NO3-). Most organic compounds in plants contain nitrogen, including amino acids, nucleic
acids, many enzymes, and energy transfer materials such as chlorophyll, ADP, and ATP. N is
necessary to produce sugars, such as in sweet, ripe fruit. Growing plants must have N to form new
cells, which plants need.

✓ Nitrogen deficiency symptoms in plants include:

o Slow-growth, stunted plants

o Yellow-green color (chlorosis)

o Firing (burnt look) of tips and margins of leaves, beginning with more mature leaves

o Low protein content of crops

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 CEA – Civil Engineering Department
CHEME – Chemistry for Engineers

✓ Symptoms of nitrogen excess include:

o Dark green, succulent, vegetative growth at the expense of seed production in grain crops, the
cost of fruit production in tomatoes and some tree crops, and the expense of sugar content in beets

o Watery potatoes

o Frost damage if there is too much succulent growth when frost hits

o Weakened stems (lodging)

o Delayed flowering or fruiting

o Boron or copper deficiency due to inhibited uptake of these nutrients

✓ Forms of nitrogen in the soil:

o Nitrogen gas in the soil air (N2)

o Nitrate (NO3-)

o Nitrite (NO2-)

o Ammonium (NH4+)

o Ammonia (NH3)

3. PHOSPHORUS (P)

✓ P is present in all living cells, including as nucleic acids (DNA and RNA), as part of phospholipid
cell membranes, and as molecules for energy storage and transfer (ATP). P also stimulates early
growth and root formation, hastens bloom time, and promotes seed production and size. It is used
in protein synthesis and is found in legume nodules.

✓ P must be balanced with N both in the plant and in the soil. In the soil, P and N compete to be
taken up. Because N is highly mobile and P is one of the least mobile nutrients, excessive N
availability can cause a P deficiency, even if there is enough P in the soil for the crop.

✓ Phosphorus deficiency symptoms in plants include:

o Slow growth, stunting

o purplish coloration on foliage of some plants

o Dark green coloration with tips of leaves dying

o Delayed maturity

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 CEA – Civil Engineering Department
CHEME – Chemistry for Engineers

4. POTASSIUM (K)

✓ Potassium plays a role in several vital processes in plants:

o Regulating the rate of photosynthesis (by activating enzymes used in photosynthesis and by
helping in the production of the energy storage molecule ATP)

o Opening and closing stomata (openings on leaves) to allow CO2 in and O2 out and to regulate
water loss

o Transporting sugars within plants, again by its role in ATP production

o Starch formation, by activating the enzyme responsible for this process

o Plant growth, by helping to produce proteins (the building blocks) and enzymes that regulate
growth

✓ Potassium deficiency symptoms in plants include:

o Slow growth

o Tip and marginal “burn” starting on more mature leaves and progressing toward the top of the
plant

o Weak stalks, plants lodge (fall over) easily

o Small fruit or shrivelled fruit and seeds

o Reduced disease and pest resistance

o Increased sensitivity to drought, frost, and salts

o White or yellow spots develop along the edges of clover leaves; in severe cases these join to give
a scorched appearance

✓ Excess potassium can cause:

o Magnesium deficiency

o Calcium deficiency in acid soils

5. CALCIUM (Ca)

✓ Calcium is an essential part of cell wall structure and must be present to form new cells throughout
the plant. Calcium also helps control movement into and out of cells by reacting with waste products
to precipitate or render them harmless to the plant.

✓ Calcium is not mobile in plants. Young tissue is affected first when there is a deficiency.

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 CEA – Civil Engineering Department
CHEME – Chemistry for Engineers

✓ Deficiency symptoms in plants include:

o Death of growing points, including on the root tips and shoot or leaf tips

o Abnormal dark green appearance of foliage

o Premature shedding of blossoms and buds

o Weakened stems because cell membranes lose permeability and disintegrate

o Blossom-end rot of tomatoes

o Short, thick, bulbous roots

✓ Plants take up Ca as an ion (Ca2+). Calcium is so abundant that it usually only needs to be added
to very acidic soils where lime is required. However, excessive irrigation can leach Ca from the soil
enough to cause plant deficiency symptoms. Excess Ca can lead to a deficiency of Mg or K.

6. MAGNESIUM (Mg)

✓ Magnesium is the central atom of chlorophyll molecules, so it is required for photosynthesis. It

also helps activate key enzymes for converting CO2 gas into carbohydrates, and many plant enzymes
are required in growth processes. Magnesium also activates enzymes necessary for P transfer within
plants.

✓ Magnesium is mobile within plants and can be translocated from older tissue to younger tissue
during deficiency conditions.

✓ Symptoms of Mg deficiency include:

o Chlorosis (yellowing) between the veins in older leaves; marginal yellowing with a green fir-tree
shape along the big midrib of the leaf

o Upward curling of leaves along their margins

o Stunted growth

o Ripe fruit is not sweet

✓ Plants take up Mg in its ionic form (Mg2+). Magnesium is generally available throughout the dry-
climate Western states, but it is often more deficient than Ca. Like Ca, Mg is easily leached, and
soils with low CEC have low Mg content. It is essential to balance Mg, K, and Ca ions so that none
of these elements dominates the CEC sites.

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 CEA – Civil Engineering Department
CHEME – Chemistry for Engineers

7. SULFUR (S)

✓ Sulfur is part of two amino acids (cysteine and methionine) incorporated into proteins. Sulfur is
also essential for nodule formation by N-fixing bacteria on the roots of legumes. It is present in oil
compounds that give plants such as garlic and onions their characteristic odor. (Vidalia onions,
known for their sweetness, come from an area with low S soils.)

✓ Sulfur deficiency problems can occur if growers rely on fertilizers that are concentrated with other
nutrients (e.g., N, P, and K) but are free of S.

✓ Symptoms of S deficiency in plants include:

o Pale young leaves, light green to yellowish in color, sometimes with veins lighter than surrounding
tissue. In some plants, older tissue may also be affected.

o Small and spindly plants

o Slow growth rate and delayed maturity

✓ Plants take up S as the sulfate ion SO42-. Sulfur is also sometimes absorbed from the air through
leaves in industrial areas where S is in high concentration.

MICRONUTRIENTS

1. BORON (B4O72-)

✓ Boron is needed in plants for:

o Synthesizing protein

o Transporting starches and sugars

o Regulating N and carbohydrate metabolism

o Root growth

o Fruit and seed formation

o Water uptake and transport

o Boron contributes more than any other micronutrient to the quality of produce.

✓ Boron is required in minute quantities by plants but may be insufficient in some soils. Boron can
also become toxic in amounts not much higher than that needed by plants. Boron toxicity is most
frequently a problem in soils formed at the bottoms of enclosed basins in arid areas where
groundwater evaporates upward through the soil, leaving salt concentrations near the surface.

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 CEA – Civil Engineering Department
CHEME – Chemistry for Engineers

2. COPPER (Cu2+)

✓ Copper is a catalyst for respiration (combusting sugars for energy in plants) and an activator of
several enzymes. It is important for carbohydrate and protein synthesis.

✓ Copper is abundant, and deficiencies rarely occur. It is found as impurities in the structures of
clay particles and other soil compounds. As these materials weather, the copper is released and
then adsorbed onto CEC sites, from which plants may take it up or leach from the soil. Consequently,
soils formed from highly weathered materials may be deficient in copper. However, since copper
can be highly toxic at low levels, amendments should not be used except where the need for it has
been established.

3. IRON (Fe2+, Fe3+)

✓ Iron plays several critical roles in plants. It is used in chlorophyll synthesis, during respiration,
and as a constituent of some enzymes and proteins. It also activates nitrogen fixation.

✓ Plants require Fe in more significant amounts than any other micronutrient. Iron is very abundant
in the soil, but some of its forms are so insoluble that plants may suffer a deficiency despite its
abundance (this would be like being stranded in the ocean yet thirsty for fresh water). This is
particularly true at pH levels above 7, where there is a high content of lime or manganese, or where
there is poor aeration. Treatment may consist of adding iron in a form that won’t be bound up in
the soil or lowering the soil pH.

4. MANGANESE (Mn2+)

✓ Manganese is part of multiple enzymes and is a catalyst of other enzymes, and so is used in the
metabolism of N and inorganic acids; for the formation of vitamins (carotene, riboflavin, and ascorbic
acid); for the assimilation of CO2 during photosynthesis; and in the breakdown of carbohydrates.

✓ Similar to Fe, high pH (over 6.5) may make Mn unavailable, as can soils very high in organic
matter (muck soils). High Mn levels may induce iron deficiency. Improving soil structure can improve
Mn availability.

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 CEA – Civil Engineering Department
CHEME – Chemistry for Engineers

5. MOLYBDENUM (MoO42-)

✓ Molybdenum is necessary for nitrogen fixation and for converting nitrate-N taken up by plants
into a form the plant can use to build amino acids and, thus, proteins. Because of this, a Mo
deficiency can cause an N deficiency in plants.

✓ As with boron, molybdenum is needed only in minute quantities and is toxic at levels above what
plants require.

6. ZINC (Zn2+)

✓ Zinc activates enzymes that run photosynthesis, helps regulate and combust carbohydrates, and
is part of synthesizing the plant hormone auxin. It is also a key for seed and grain maturation and
production.

✓ Soils formed from highly weathered materials may be deficient in Zn, while soils formed from
igneous rocks tend to have higher levels of Zn. Warm soil temperatures improve Zn availability, as
does well-aerated soil. High levels of available P can cause Zn deficiency in plants.

7. CHLORINE (Cl-)

✓ Chlorine is required for photosynthetic reactions in plants. However, the quantities needed are so
small that deficiencies are rare, usually in places with high rainfall and sandy soils, where Cl anions
would leach out.

ORGANIC MATTER

Many pleasant drives in the country have been affected when the passengers of a car are hit with
an unpleasant but familiar odor. Many people complain about the smell without questioning why it
exists. There is a very good reason for this practice. Although they are often given more unpleasant
names, these animal wastes are known as organic fertilizers. These fertilizers have a very high
content of organic matter. Organic matter is a dead, decaying matter originating from a living
source. It prevents nutrients from being lost from the soil by binding these nutrients. Therefore, the
best soil for crop production will have a very high organic content. Most organic fertilizer originates
from livestock such as cows, pigs, and poultry. Compost is also an organic fertilizer. Compost
comprises grass clippings, table scraps, ashes, seaweed, and many other food products. Organic

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 CEA – Civil Engineering Department
CHEME – Chemistry for Engineers

fertilizers contain high levels of Nitrogen and moderate levels of Phosphorus and Potassium. The
nutrient content of organic fertilizer can vary according to the animal that produced it. Spreading
organic fertilizers allows farmers to rid themselves of accumulated livestock waste. It also provides
farmers with a free source of fertilizer, which is sometimes sufficient to meet the needs of the
desired crop. Organic fertilizers are also less harmful to the environment. This may be one of the
first recycling practices that ever developed.

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